Conservators at the Art Institute of Chicago wanted to solve the mystery of the missing pigment.

They were looking at “Madame Léon Clapisson,” an 1883 portrait by the French impressionist Pierre-Auguste Renoir, which had just been removed from its frame for detailed study. The part that had been hidden behind the frame was markedly more vivid.

“It’s been protected from light, so we were able to really appreciate the original color in this unfaded area,” said Francesca Casadio, the museum’s senior conservation scientist. “It’s really quite striking. It’s a very scarlet-purple kind of paint.”

Although the bright edges were observed about 15 years ago, the museum did not have the scientific facilities then to investigate. But four years ago, a project to create a digital catalog of the museum’s Renoir holdings provided an opportunity to run a battery of scientific tests.

Kelly Keegan, the conservator working on the project, said a look under the microscope quickly revealed that the color shift was not a revision by Renoir himself or caused by imprudent cleaning.

“It’s very clear it’s original paint,” she said. “You can see there are particles on the surface that are sort of translucent now.”

The unfaded edges did not have the translucent particles, which evidently contained pigment molecules that had fallen apart, losing their color.

Conservators at museums around the world regularly bathe their paintings with light of different wavelengths — infrared, ultraviolet, X-rays — to see what might be hidden on or beneath the surface. But those techniques cannot identify organic pigments, extracted from plants and insects, which were popular with the impressionists. For that, Casadio and Federica Pozzi, both conservation scientists who were trained as chemists, had begun using a laser technique called surface-enhanced Raman spectroscopy.

When the laser hits a material, photons bounce off it, some of them inducing vibrations in the molecules and shifting the photons’ wavelengths. The spectrum of colors in the scattered light serves as a fingerprint to identify the molecules. In surface-enhanced Raman spectroscopy, the sample is laid on silver nanoparticles, which act as an antenna to amplify the signal.

Using a minuscule red speck scraped from the painting’s edge, the scientists identified the pigment: carmine lake, made from crushed and ground cochineal insects that live on cactuses in Mexico and South America. The striking red color had evidently caught Renoir’s eye.

But it does not last.

Even paint catalogs of the era noted that the color wasn’t stable when exposed to light.

Ground-up cochineal is still used today, but as a natural coloring in foods like candy, in which longevity is not a requirement. Starbucks used to add it to some of its drinks but stopped in 2012 after complaints from vegetarians.

There are no thoughts of trying to restore the portrait to its original hues, but with computer software Keegan was able to create a digital version of how it might have looked in 1883.

The cool background of grays, blues and greens was instead a hotter swath of red and purple — “in some ways, more daring, more adventurous,” said Gloria Groom, the museum’s senior curator. “It’s so weird. You think you know an artist, and then science tells something different about him and you’re like, ‘Oh, well, that doesn’t fit my idea of what this artist is.’ ”

Keegan said that even though her digital version did not alter the colors of Clapisson’s face, someone looking at the painting would perceive it as different.

“It brings out all the rosy quality to her flesh,” she said. “She looks younger.”

“Madame Léon Clapisson” is not the only painting to change color over the years. A few days ago, conservators found a deeper, more intense red on the sleeve of one of the children in Paul Gauguin’s “Polynesian Woman With Children” — again, part of the canvas that had been protected by the frame.

“This could be a very similar fading phenomenon,” Pozzi said.

Zinc yellow paint used in the most famous work at the Art Institute, Georges Seurat’s “A Sunday Afternoon on the Island of la Grande Jatte,” was also unstable, turning from bright lemon to drab ocher. In that case, an art critic noticed the change within a few years, lamenting that some of the color had drained out.

Groom has looked for similar complaints about “Madame Léon Clapisson,” which Renoir put on public display several times, and did not find any. “It seems like if it really faded quickly, then someone would have said, ‘Oh, I saw this three years ago, didn’t look like that,’ ” she said.